Dear AMBER Developers,
I am currently working with the 1D-RISM/3D-RISM workflow in AmberTools and
encountered an issue related to the generation of the .xvv file when
modifying solvent charges.
Problem Description:
I modified the partial charges in the solvent .mdl file (specifically for a
[electrolyte] model, e.g., KCl with scaled charges). However, after running
rism1d to generate the .xvv file, the resulting file does not appear to
reflect the updated charges.
Steps Performed:
Edited the .mdl file to reduce/scale the charges of solvent sites.
Verified that the modified .mdl file is referenced correctly in the rism1d
input (model field under species).
Removed any existing restart files (*.sav) to avoid reuse of previous
solutions.
Re-ran rism1d to regenerate the .xvv file.
Checked the %FLAG QV section in the generated .xvv, but the values appear
unchanged (or not consistent with the modified charges).
Observations:
The output .xvv seems identical (or very similar) to the one generated
using the original charges.
This behavior persists even after removing restart files and regenerating
all outputs.
I am using the KH closure (though I understand the closure should not
affect whether charges propagate).
Questions:
Are there additional steps required to ensure that modified .mdl charges
are propagated into the .xvv file?
Could there be any caching, internal defaults, or preprocessing that
overrides .mdl charges?
Is there a recommended way to verify that the updated interaction
potentials (from modified charges) are actually being used during the
1D-RISM calculation?
Are there known issues or best practices when working with scaled-charge
electrolyte models in RISM?
System Details:
Amber version : 20, force field ff14SB and TIP3P water model
I would greatly appreciate any guidance or suggestions to resolve this
issue. Please let me know if you would like me to share input/output files
for further inspection.
Thank you for your time and support.
Best regards,
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Received on Wed Mar 18 2026 - 19:00:03 PDT
